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r342: bugfix in bwasw - AS is off by one 

but I do not understand why the old code does not have the same problem.
This commit is contained in:
Heng Li 2013-03-08 12:06:45 -05:00
parent b5b50ac8da
commit 017be45407
3 changed files with 3 additions and 6 deletions
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5
Makefile
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@ -1,8 +1,7 @@
CC= gcc CC= gcc
CFLAGS= -g -Wall -O2 CFLAGS= -g -Wall -O2
CXXFLAGS= $(CFLAGS)
AR= ar AR= ar
DFLAGS= -DHAVE_PTHREAD #-D_NO_SSE2 #-D_FILE_OFFSET_BITS=64 DFLAGS= -DHAVE_PTHREAD
LOBJS= utils.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o LOBJS= utils.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o
AOBJS= QSufSort.o bwt_gen.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \ AOBJS= QSufSort.o bwt_gen.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
is.o bwtindex.o bwape.o kopen.o pemerge.o \ is.o bwtindex.o bwape.o kopen.o pemerge.o \
@ -17,8 +16,6 @@ SUBDIRS= .
.c.o: .c.o:
$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
.cc.o:
$(CXX) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
all:$(PROG) all:$(PROG)

2
bwtsw2_aux.c
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@ -153,7 +153,7 @@ void bsw2_extend_rght(const bsw2opt_t *opt, bwtsw2_t *b, uint8_t *query, int lq,
for (k = p->k, j = 0; k < p->k + lt && k < l_pac; ++k) for (k = p->k, j = 0; k < p->k + lt && k < l_pac; ++k)
target[j++] = pac[k>>2] >> (~k&3)*2 & 0x3; target[j++] = pac[k>>2] >> (~k&3)*2 & 0x3;
lt = j; lt = j;
score = ksw_extend(lq - p->beg, &query[p->beg], lt, target, 5, mat, opt->q, opt->r, opt->bw, -1, 1, &qle, &tle, 0, 0, 0); score = ksw_extend(lq - p->beg, &query[p->beg], lt, target, 5, mat, opt->q, opt->r, opt->bw, -1, 1, &qle, &tle, 0, 0, 0) - 1;
// if (score < p->G) fprintf(stderr, "[bsw2_extend_hits] %d < %d\n", score, p->G); // if (score < p->G) fprintf(stderr, "[bsw2_extend_hits] %d < %d\n", score, p->G);
if (score >= p->G) { if (score >= p->G) {
p->G = score; p->G = score;

2
main.c
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@ -3,7 +3,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.0-r341-beta" #define PACKAGE_VERSION "0.7.0-r342-beta"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);